Can Freestyle Visibility accuracy be improved?
As far as I can see, you do have a loss of precision .. due to the topology of your model.

Your model has many, many duplicate vertices.. they have to go first.(M Merge &gt; By Distance)
But even then, the topology is very extreme, in places. The only fixed data-points the renderer has to work with are vertex locations. The rest is interpolation - of normals, shading-point locations, everything. If a rendered polygon is a very long thin triangle, then you're running into interpolation inaccuracies near its center.

Flat surfaces are OK, interpolating between a value and itself doesn't present a problem.
As a quick hack, subdividing the surface of the long shafts restored their opacity to Freestyle, but a repair of the topology would make a better job of it. You might get away with replacing the shafts  with dimensioned, quad-based cylinders, with a few subdivisions of their length.
Raising the nuts so their bottom edges are at/slightly above the plate they are  screwed down onto, makes them visible to Freestyle without changing the edge selection settings. (Some are buried at the moment)
Introducing per-face-vertex normals, by switching 'Autosmooth' on, with appropriate, (quite high for these elements,) threshold angles, will help keep smooth shading without overdoing the poly-count.